User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.4k
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Italy
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@jotsetung
Last seen:
2 weeks, 3 days ago
Joined:
4 years, 5 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 265 results • page 1 of 27 • next >
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Comment: C: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
... Just a small comment to James' excellent answer: if your alignment/gene annotations were based on a specific Ensembl release, you should also ensure that you are loading/adding annotations from the same release. Example, your object is based on Ensembl release 91 data, then you would want to get the ...
written 17 days ago by Johannes Rainer1.4k
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Comment: C: mzR unable to open uncorrupted mzXML file
... Before digging into the error message I would make sure that you have all the most recent package versions and that all files are really there. So, please run `BiocManager::install()` to update potentially outdated packages and then `all(file.exists(files))`. You say you have ~ 1500 files, so mayb ...
written 22 days ago by Johannes Rainer1.4k
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Job: Postdoctoral researcher in Computational Metabolomics
... Dear all, Eurac Research is looking for a ## Postdoctoral researcher in Computational Metabolomics The Institute for Biomedicine is seeking a highly motivated researcher to join the Computational Metabolomics team. The Institute for Biomedicine is home to an international and interdisciplinary te ...
metabolomics xcms job written 7 weeks ago by Johannes Rainer1.4k
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Comment: C: How to use EnsDb in annotatePeak from package "ChIPseeker"
... `intronsByTranscript` is exported in ensembldb version 2.6.6 which will be available in a few days. ...
written 8 weeks ago by Johannes Rainer1.4k
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Answer: A: How to use EnsDb in annotatePeak from package "ChIPseeker"
... The reason is that `ensembldb` doesn't have an `intronsByTranscript` method. I'll add that and it *should* work. cheers, jo ...
written 8 weeks ago by Johannes Rainer1.4k
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Answer: A: Retrieve canonical transcript for each gene via ensembldb R package
... At present I am not including this information to the ensembldb databases. So there is no way to get the canonical transcript for a gene using ensembldb. Sorry for that. ...
written 12 weeks ago by Johannes Rainer1.4k
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Comment: C: Troubles with mzR and BiocInstaller
... Also, the message is rather a warning than an error. mzR will most likely work as expected.   ...
written 4 months ago by Johannes Rainer1.4k
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Comment: C: make TxDb from list of genes
... I agree with James. No need to create a new TxDb database. You could simply subset an EnsDb database to your list of input genes (even better if you have Ensembl IDs): assuming you have your Ensembl gene IDs in a variable called ensids: library(EnsDb.Hsapiens.v86) edb <- filter(EnsDb.Hsapiens.v ...
written 4 months ago by Johannes Rainer1.4k
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Answer: A: Pick coding vs non-coding from Ensembl data set
... You can simply filter the complete EnsDb database to contain only protein coding genes or all other genes (note: this includes miRNA genes, lincRNAs, pseudogenes, snoRNA, scaRNA, sRNA, scRNA, rRNA ...). > library(EnsDb.Hsapiens.v86) > ## Filter the EnsDb database for protein coding genes > ...
written 4 months ago by Johannes Rainer1.4k
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Comment: C: Ensembl plants at annotationHub?
... I've generated the EnsDb. You can get the file from here https://www.dropbox.com/sh/wglt28zlfzhjubs/AADzGqJ0zydKRmdqbOsH_Ru5a?dl=0 after unzipping you can simply load the sqlite file with edb <- EnsDb(<sqlite-file>)   ...
written 4 months ago by Johannes Rainer1.4k

Latest awards to Johannes Rainer

Scholar 5 months ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 5 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 5 months ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 5 months ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Popular Question 6 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 7 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 10 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 10 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Scholar 22 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 22 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 22 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 22 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 22 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 22 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 22 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 22 months ago, received more than 100 upvotes.
Voter 22 months ago, voted more than 100 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 22 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 22 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 23 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 2.0 years ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Scholar 2.0 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype

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